It is easiest for me to think about this in terms of sine waves. Fourier says that any signal can be represented as a sum of sine waves. So a complex sound can be thought of as a bunch of sine waves of various amplitudes and phases stacked on top of eachother. Each sine wave has a different wavelength, so when you use multiple microphones for a single source, some frequencies will arrive at one microphone at a certain phase but arrive at a different phase in the other microphone, depending on distance. Therefore it is impossible to get every component (every sine wave) aligned because each sinusoidal component is possibly in a different phase of it's cycle compared to the other microphone. So if you visually nudge the waveform of the distant kick mic to play earlier (in a DAW), to match the closer mic'ed waveform, the lowest frequency component might be aligned but the higher frequencies will be randomly in or out of phase... Which as we know creates a chorusing and or comb filtering effect.

Inverting the waveform is similar, but sounds different. There is no perfect way to do this. I believe the first instinct is usually to just flip the phase because historically it was cheaper, and it is a fast way to A/B the results of tampering with the phase.